Variant report

Variant	rs2198478
Chromosome Location	chr2:210366371-210366372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:210363883..210366615-chr2:210368582..210372932,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10173260	0.95[ASN][1000 genomes]
rs10208979	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1031461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs10737939	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10737940	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs11686346	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11687844	0.99[ASN][1000 genomes]
rs12052799	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12053460	0.93[ASN][1000 genomes]
rs12614974	0.88[CEU][hapmap]
rs12623404	0.88[CEU][hapmap]
rs2123700	0.98[ASN][1000 genomes]
rs2198475	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2198476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2365657	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365658	0.96[ASN][1000 genomes]
rs2710477	0.86[CEU][hapmap]
rs288046	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288062	1.00[ASN][1000 genomes]
rs288064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs288065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs288068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886435	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2886436	0.95[ASN][1000 genomes]
rs4672554	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4673481	0.93[ASN][1000 genomes]
rs4673482	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6435530	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[ASN][1000 genomes]
rs6435531	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6728378	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6738205	0.93[ASN][1000 genomes]
rs6740822	0.99[ASN][1000 genomes]
rs7559831	0.94[ASN][1000 genomes]
rs7561678	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7562585	0.94[ASN][1000 genomes]
rs7568354	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7574854	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580512	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7586196	0.98[ASN][1000 genomes]
rs7593377	0.96[ASN][1000 genomes]
rs7601095	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs852734	0.98[ASN][1000 genomes]
rs9288409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs997109	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834518	chr2:210204958-210372744	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv834519	chr2:210271017-210400153	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210360200-210366400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:210361800-210376400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:210363600-210370800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:210363600-210378400	Weak transcription	Brain Germinal Matrix	brain
5	chr2:210364600-210387600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:210364600-210392200	Weak transcription	Pancreas	Pancrea
7	chr2:210365200-210369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:210365400-210368600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:210366000-210366400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:210366200-210366400	Enhancers	Aorta	Aorta
11	chr2:210366200-210366600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:210366200-210366600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:210366200-210366600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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